For genesis or other cases maybe the best option is a different option in "General" section for vertical art? Unsure about the video snaps working on that though. 
I plan to do something like this: a "dummy" hidden boxart will be used to get the proportions, if it's almost square then square mode is triggered, if it's horizontal or vertical then Arcadeflow will use horizontal or vertical thumbs.
I'll ditch videos in this case, but you'll see them in the "history" page.
Controlling different boxart or flyers dimensions can be hard. I'm giving a little help to the Chicuelo port regarding some extra layout options for vertical art like flyers or boxart like the NES, Saturn, PS2, etc., other for SNES and one for square art. It can get tricky and hard. 
So probably best is to have extra layout options for anyone that wants them (similar to Display menu), with default one being the arcade version using snaps?
It's not hard per se, it's just that I don't want to add another shader surface stack to dynamically generate shadows, and my shadows are only 4:3, 3:4 or square, but that should fit most cases

As far as options are concerned, I plan to do like this: Arcadeflow will always work in Arcade mode, showing console games in 4:3 aspect ratio (GameBoy will be cropped but it's ok). There will be an optional "boxart" mode that will make console games show boxarts, and arcade game won't be affected.
The issue is that ALL console displays will be affected by that choice, but I hope in the future we'll be able to have per-display layout settings.